Low Resolution Refinement of Atomic Models Against Crystallographic Data

2017 ◽  
pp. 565-593 ◽  
Author(s):  
Robert A. Nicholls ◽  
Oleg Kovalevskiy ◽  
Garib N. Murshudov
Keyword(s):  
Crystallographic Data ◽  
Low Resolution ◽  
Atomic Models

Low-Resolution Density Maps from Atomic Models: How Stepping “Back” Can Be a Step “Forward”

1999 ◽  
Vol 125 (2-3) ◽  
pp. 166-175 ◽  
Author(s):  
David M. Belnap ◽  
Abhinav Kumar ◽  
Jon T. Folk ◽  
Thomas J. Smith ◽  
Timothy S. Baker
Keyword(s):  
Low Resolution ◽  
Atomic Models ◽  
Density Maps

scholarly journals Automatic Inference of Sequence from Low-Resolution Crystallographic Data

Structure ◽  
2018 ◽  
Vol 26 (11) ◽  
pp. 1546-1554.e2
Author(s):  
Ziv Ben-Aharon ◽  
Michael Levitt ◽  
Nir Kalisman
Keyword(s):  
Crystallographic Data ◽  
Low Resolution ◽  
Automatic Inference

scholarly journals Model-building strategies for low-resolution X-ray crystallographic data

2009 ◽  
Vol 65 (2) ◽  
pp. 121-127 ◽  
Author(s):  
Anjum M. Karmali ◽  
Tom L. Blundell ◽  
Nicholas Furnham
Keyword(s):  
Model Building ◽  
Crystallographic Data ◽  
Low Resolution ◽  
X Ray

scholarly journals Real-space refinement in Phenix for cryo-EM and crystallography

2018 ◽  
Author(s):  
Pavel V. Afonine ◽  
Billy K. Poon ◽  
Randy J. Read ◽  
Oleg V. Sobolev ◽  
Thomas C. Terwilliger ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Target Function ◽  
Real Space ◽  
Molecular Symmetry ◽  
Low Resolution ◽  
Fast Calculation ◽  
Additional Information ◽  
Extra Information ◽  
Atomic Models ◽  
Resolution Data

AbstractThis article describes the implementation of real-space refinement in the phenix.real_space_refine program from the Phenix suite. Use of a simplified refinement target function enables fast calculation, which in turn makes it possible to identify optimal data-restraints weight as part of routine refinements with little runtime cost. Refinement of atomic models against low-resolution data benefits from the inclusion of as much additional information as is available. In addition to standard restraints on covalent geometry, phenix.real_space_refine makes use of extra information such as secondary-structure and rotamer-specific restraints, as well as restraints or constraints on internal molecular symmetry. Re-refinement of 385 cryo-EM derived models available in the PDB at resolutions of 6 Å or better shows significant improvement of models and the fit of these models to the target maps.SynopsisA description of the implementation of real-space refinement in the phenix.real_space_refine program from the Phenix suite and its application to re-refinement of cryo-EM derived models.

scholarly journals TEMPy: a Python library for assessment of three-dimensional electron microscopy density fits

2015 ◽  
Vol 48 (4) ◽  
pp. 1314-1323 ◽  
Author(s):  
Irene Farabella ◽  
Daven Vasishtan ◽  
Agnel Praveen Joseph ◽  
Arun Prasad Pandurangan ◽  
Harpal Sahota ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Three Dimensional ◽  
Dimensional Electron ◽  
Low Resolution ◽  
Macromolecular Assemblies ◽  
Atomic Models ◽  
Density Maps ◽  
Consensus Scoring ◽  
Ensemble Generation ◽  
Modular Nature

Three-dimensional electron microscopy is currently one of the most promising techniques used to study macromolecular assemblies. Rigid and flexible fitting of atomic models into density maps is often essential to gain further insights into the assemblies they represent. Currently, tools that facilitate the assessment of fitted atomic models and maps are needed.TEMPy(template and electron microscopy comparison using Python) is a toolkit designed for this purpose. The library includes a set of methods to assess density fits in intermediate-to-low resolution maps, both globally and locally. It also provides procedures for single-fit assessment, ensemble generation of fits, clustering, and multiple and consensus scoring, as well as plots and output files for visualization purposes to help the user in analysing rigid and flexible fits. The modular nature ofTEMPyhelps the integration of scoring and assessment of fits into large pipelines, making it a tool suitable for both novice and expert structural biologists.

Caricaturing as a general method to improve poor face recognition: Evidence from low-resolution images, other-race faces, and older adults.

2019 ◽  
Vol 25 (2) ◽  
pp. 256-279 ◽  
Author(s):  
Amy Dawel ◽  
Tsz Ying Wong ◽  
Jodie McMorrow ◽  
Callin Ivanovici ◽  
Xuming He ◽  
...  
Keyword(s):  
Older Adults ◽  
Face Recognition ◽  
Low Resolution ◽  
General Method ◽  
Low Resolution Images
Sign in / Sign up

Export Citation Format

Share Document